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Urtasun-Elizari JM, Ma R, Pickford H, Farrell D, Gonzalez G, Perets V, Nakajima C, Suzuki Y, MacHugh DE, Bhatt A, Gordon SV. Functional analysis of the Mycobacterium bovis AF2122/97 PhoPR system. Tuberculosis (Edinb) 2024; 148:102544. [PMID: 39018651 DOI: 10.1016/j.tube.2024.102544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
The PhoPR system is a master regulator in Mycobacterium tuberculosis. A key difference between M. tuberculosis and Mycobacterium bovis is a G71I substitution in the M. bovis PhoR orthologue. Functional studies of the M. bovis PhoPR system have generated conflicting findings, with some research suggesting that the M. bovis PhoPR is defective while others indicate it is functional. We sought to revisit the functionality of the M. bovis PhoPR system. To address this, we constructed a phoPR mutant in the reference strain M. bovis AF2122/97. We employed a combination of growth assays and transcriptomics analyses to assess the phenotype of the mutant vs wild type and complemented strains. We found that the M. bovis AF2122/97 ΔphoPR mutant showed a growth defect on solid and liquid media compared to the wild type and complemented strains. The transcriptome of the M. bovis AF2122/97 ΔphoPR mutant was also altered as compared to wild type, including differential expression of genes involved in lipid metabolism and secretion. Our work provides further insight into the activity of PhoPR in M. bovis and underlines the importance of the PhoPR system as a master regulator of gene expression in the Mycobacterium tuberculosis complex.
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Affiliation(s)
| | - Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Hayleah Pickford
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Gabriel Gonzalez
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan
| | - Viktor Perets
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Chie Nakajima
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
| | - Yasuhiko Suzuki
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
| | - David E MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Centre for One Health, University College Dublin, Belfield, Dublin, Ireland
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan; UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Centre for One Health, University College Dublin, Belfield, Dublin, Ireland; UCD Centre for Experimental Pathogen Host Research, University College Dublin, Belfield, Dublin, Ireland.
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2
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Fang WW, Kong XL, Yang JY, Tao NN, Li YM, Wang TT, Li YY, Han QL, Zhang YZ, Hu JJ, Li HC, Liu Y. PE/PPE mutations in the transmission of Mycobacterium tuberculosis in China revealed by whole genome sequencing. BMC Microbiol 2024; 24:206. [PMID: 38858614 PMCID: PMC11163795 DOI: 10.1186/s12866-024-03352-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/26/2024] [Indexed: 06/12/2024] Open
Abstract
OBJECTIVE This study aims to examine the impact of PE/PPE gene mutations on the transmission of Mycobacterium tuberculosis (M. tuberculosis) in China. METHODS We collected the whole genome sequencing (WGS) data of 3202 M. tuberculosis isolates in China from 2007 to 2018 and investigated the clustering of strains from different lineages. To evaluate the potential role of PE/PPE gene mutations in the dissemination of the pathogen, we employed homoplastic analysis to detect homoplastic single nucleotide polymorphisms (SNPs) within these gene regions. Subsequently, logistic regression analysis was conducted to analyze the statistical association. RESULTS Based on nationwide M. tuberculosis WGS data, it has been observed that the majority of the M. tuberculosis burden in China is caused by lineage 2 strains, followed by lineage 4. Lineage 2 exhibited a higher number of transmission clusters, totaling 446 clusters, of which 77 were cross-regional clusters. Conversely, there were only 52 transmission clusters in lineage 4, of which 9 were cross-regional clusters. In the analysis of lineage 2 isolates, regression results showed that 4 specific gene mutations, PE4 (position 190,394; c.46G > A), PE_PGRS10 (839,194; c.744 A > G), PE16 (1,607,005; c.620T > G) and PE_PGRS44 (2,921,883; c.333 C > A), were significantly associated with the transmission of M. tuberculosis. Mutations of PE_PGRS10 (839,334; c.884 A > G), PE_PGRS11 (847,613; c.1455G > C), PE_PGRS47 (3,054,724; c.811 A > G) and PPE66 (4,189,930; c.303G > C) exhibited significant associations with the cross-regional clusters. A total of 13 mutation positions showed a positive correlation with clustering size, indicating a positive association. For lineage 4 strains, no mutations were found to enhance transmission, but 2 mutation sites were identified as risk factors for cross-regional clusters. These included PE_PGRS4 (338,100; c.974 A > G) and PPE13 (976,897; c.1307 A > C). CONCLUSION Our results indicate that some PE/PPE gene mutations can increase the risk of M. tuberculosis transmission, which might provide a basis for controlling the spread of tuberculosis.
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Affiliation(s)
- Wei-Wei Fang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Xiang-Long Kong
- Shandong Artificial Intelligence Institute, Qilu University of Technology & Shandong Academy of Sciences, Jinan, Shandong, PR China
| | - Jie-Yu Yang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Ning-Ning Tao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
| | - Ya-Meng Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Ting-Ting Wang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
| | - Ying-Ying Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Qi-Lin Han
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Yu-Zhen Zhang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Jin-Jiang Hu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Huai-Chen Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China.
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3
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Hiza H, Zwyer M, Hella J, Arbués A, Sasamalo M, Borrell S, Xu ZM, Ross A, Brites D, Fellay J, Reither K, Gagneux S, Portevin D. Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania. Sci Rep 2024; 14:9287. [PMID: 38653771 DOI: 10.1038/s41598-024-60001-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) comprises nine human-adapted lineages that differ in their geographical distribution. Local adaptation of specific MTBC genotypes to the respective human host population has been invoked in this context. We aimed to assess if bacterial genetics governs MTBC pathogenesis or if local co-adaptation translates into differential susceptibility of human macrophages to infection by different MTBC genotypes. We generated macrophages from cryopreserved blood mononuclear cells of Tanzanian tuberculosis patients, from which the infecting MTBC strains had previously been phylogenetically characterized. We infected these macrophages ex vivo with a phylogenetically similar MTBC strain ("matched infection") or with strains representative of other MTBC lineages ("mismatched infection"). We found that L1 infections resulted in a significantly lower bacterial burden and that the intra-cellular replication rate of L2 strains was significantly higher compared the other MTBC lineages, irrespective of the MTBC lineage originally infecting the patients. Moreover, L4-infected macrophages released significantly greater amounts of TNF-α, IL-6, IL-10, MIP-1β, and IL-1β compared to macrophages infected by all other strains. While our results revealed no measurable effect of local adaptation, they further highlight the strong impact of MTBC phylogenetic diversity on the variable outcome of the host-pathogen interaction in human tuberculosis.
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Affiliation(s)
- Hellen Hiza
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Michaela Zwyer
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jerry Hella
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Ainhoa Arbués
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Mohamed Sasamalo
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Zhi Ming Xu
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Amanda Ross
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sébastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Damien Portevin
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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Li YF, Yang Y, Kong XL, Song WM, Li YM, Li YY, Fang WW, Yang JY, Men D, Yu CB, Yang GR, Han WG, Liu WY, Yan K, Li HC, Liu Y. Transmission dynamics and phylogeography of Mycobacterium tuberculosis in China based on whole-genome phylogenetic analysis. Int J Infect Dis 2024; 140:124-131. [PMID: 37863309 DOI: 10.1016/j.ijid.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/30/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
OBJECTIVES This study aimed to describe the lineage-specific transmissibility and epidemiological migration of Mycobacterium tuberculosis in China. METHODS We curated a large set of whole-genome sequences from 3204 M. tuberculosis isolates, including thousands of newly sequenced genomes, and applied a series of metrics to compare the transmissibility of M. tuberculosis strains between lineages and sublineages. The countrywide transmission patterns of major lineages were explored. RESULTS We found that lineage 2 (L2) was the most prevalent lineage in China (85.7%), with the major sublineage 2.2.1 (80.9%), followed by lineage 4 (L4) (13.8%), which comprises major sublineages 4.2 (1.5%), 4.4 (6.2%) and 4.5 (5.8%). We showed evidence for frequent cross-regional spread and large cluster formation of L2.2.1 strains, whereas L4 strains were relatively geographically restricted in China. Next, we applied a series of genomic indices to evaluate M. tuberculosis strain transmissibility and uncovered higher transmissibility of L2.2.1 compared with the L2.2.2 and L4 sublineages. Phylogeographic analysis showed that southern, eastern, and northern China were highly connected regions for countrywide L2.2.1 strain spread. CONCLUSIONS The present study provides insights into the different transmission and migration patterns of the major M. tuberculosis lineages in China and highlights that transmissible L2.2.1 is a threat to tuberculosis control.
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Affiliation(s)
- Yi-Fan Li
- Department of Respiratory and Critical Care Medicine, the Third Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, PR China
| | - Yang Yang
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao, PR China
| | - Xiang-Long Kong
- Xiang-long Kong, Shandong Artificial Intelligence Institute Qilu University of Technology & Shandong Academy of Sciences, Jinan, Shandong, PR China
| | - Wan-Mei Song
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Ya-Meng Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China; Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Ying-Ying Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China; Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Wei-Wei Fang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Jie-Yu Yang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Dan Men
- College of Geography and Environmental Science, Northwest Normal University, No. 967 Anning East Road, Lanzhou, Gansu Province, China
| | - Chun-Bao Yu
- Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center, Jinan, Shandong, PR China
| | - Guo-Ru Yang
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Wen-Ge Han
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Wen-Yu Liu
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Kun Yan
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Huai-Chen Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China.
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5
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Orgeur M, Sous C, Madacki J, Brosch R. Evolution and emergence of Mycobacterium tuberculosis. FEMS Microbiol Rev 2024; 48:fuae006. [PMID: 38365982 PMCID: PMC10906988 DOI: 10.1093/femsre/fuae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged by clonal expansion from a pool of recombinogenic Mycobacterium canettii-like tubercle bacilli. A better understanding of how MTBC populations evolved from less virulent mycobacteria may allow for discovering improved TB control strategies and future epidemiologic trends. In this review, we highlight new insights into the evolution of mycobacteria at the genus level, describing different milestones in the evolution of mycobacteria, with a focus on the genomic events that have likely enabled the emergence and the dominance of the MTBC. We also review the recent literature describing the various MTBC lineages and highlight their particularities and differences with a focus on host preferences and geographic distribution. Finally, we discuss on putative mechanisms driving the evolution of tubercle bacilli and mycobacteria in general, by taking the mycobacteria-specific distributive conjugal transfer as an example.
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Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Camille Sous
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Jan Madacki
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Unit for Human Evolutionary Genetics, 75015 Paris, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
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Belardinelli JM, Arora D, Avanzi C, Wheat WH, Bryant JM, Spencer JS, Blundell TL, Parkhill J, Floto RA, Jackson M. Clinically relevant mutations in the PhoR sensor kinase of host-adapted Mycobacterium abscessus isolates impact response to acidic pH and virulence. Microbiol Spectr 2023; 11:e0158823. [PMID: 37874174 PMCID: PMC10715180 DOI: 10.1128/spectrum.01588-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/14/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Difficult-to-treat pulmonary infections caused by nontuberculous mycobacteria of the Mycobacterium abscessus group have been steadily increasing in the USA and globally. Owing to the relatively recent recognition of M. abscessus as a human pathogen, basic and translational research to address critical gaps in diagnosis, treatment, and prevention of diseases caused by this microorganism has been lagging behind that of the better-known mycobacterial pathogen, Mycobacterium tuberculosis. To begin unraveling the molecular mechanisms of pathogenicity of M. abscessus, we here focus on the study of a two-component regulator known as PhoPR which we found to be under strong evolutionary pressure during human lung infection. We show that PhoPR is activated at acidic pH and serves to regulate a defined set of genes involved in host adaptation. Accordingly, clinical isolates from chronically infected human lungs tend to hyperactivate this regulator enabling M. abscessus to escape macrophage killing.
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Affiliation(s)
- Juan M Belardinelli
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University , Fort Collins, Colorado, USA
| | - Divya Arora
- Department of Medicine, Molecular Immunity Unit, University of Cambridge, MRC-Laboratory of Molecular Biology , Cambridge, United Kingdom
| | - Charlotte Avanzi
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University , Fort Collins, Colorado, USA
| | - William H Wheat
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University , Fort Collins, Colorado, USA
| | - Josephine M Bryant
- Department of Medicine, Molecular Immunity Unit, University of Cambridge, MRC-Laboratory of Molecular Biology , Cambridge, United Kingdom
- University of Cambridge Centre for AI in Medicine , Cambridge, United Kingdom
| | - John S Spencer
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University , Fort Collins, Colorado, USA
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge , Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Sanger Institute , Hinxton, United Kingdom
- Department of Veterinary Medicine, University of Cambridge , Cambridge, United Kingdom
| | - R Andres Floto
- Department of Medicine, Molecular Immunity Unit, University of Cambridge, MRC-Laboratory of Molecular Biology , Cambridge, United Kingdom
- University of Cambridge Centre for AI in Medicine , Cambridge, United Kingdom
- Cambridge Centre for Lung Infection, Papworth Hospital , Cambridge, United Kingdom
| | - Mary Jackson
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University , Fort Collins, Colorado, USA
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7
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Yenew B, Ghodousi A, Diriba G, Tesfaye E, Cabibbe AM, Amare M, Moga S, Alemu A, Dagne B, Sinshaw W, Mollalign H, Meaza A, Tadesse M, Gamtesa DF, Abebaw Y, Seid G, Zerihun B, Getu M, Chiacchiaretta M, Gaudin C, Marceau M, Didelot X, Tolera G, Abdella S, Kebede A, Getahun M, Mehammed Z, Supply P, Cirillo DM. A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex. Nat Commun 2023; 14:7519. [PMID: 37980337 PMCID: PMC10657438 DOI: 10.1038/s41467-023-42755-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 10/18/2023] [Indexed: 11/20/2023] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.
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Affiliation(s)
- Bazezew Yenew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Arash Ghodousi
- Vita-Salute San Raffaele University, Milan, Italy.
- IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Getu Diriba
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ephrem Tesfaye
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Misikir Amare
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Shewki Moga
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ayinalem Alemu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Binyam Dagne
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | - Abyot Meaza
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | | | - Getachew Seid
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Melak Getu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Cyril Gaudin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Michael Marceau
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, CV4 7AL, Coventry, UK
| | | | - Saro Abdella
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Abebaw Kebede
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France.
| | - Daniela Maria Cirillo
- Vita-Salute San Raffaele University, Milan, Italy.
- IRCCS San Raffaele Scientific Institute, Milan, Italy.
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8
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Seah YM, Stewart MK, Hoogestraat D, Ryder M, Cookson BT, Salipante SJ, Hoffman NG. In Silico Evaluation of Variant Calling Methods for Bacterial Whole-Genome Sequencing Assays. J Clin Microbiol 2023; 61:e0184222. [PMID: 37428072 PMCID: PMC10446864 DOI: 10.1128/jcm.01842-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/18/2023] [Indexed: 07/11/2023] Open
Abstract
Identification and analysis of clinically relevant strains of bacteria increasingly relies on whole-genome sequencing. The downstream bioinformatics steps necessary for calling variants from short-read sequences are well-established but seldom validated against haploid genomes. We devised an in silico workflow to introduce single nucleotide polymorphisms (SNP) and indels into bacterial reference genomes, and computationally generate sequencing reads based on the mutated genomes. We then applied the method to Mycobacterium tuberculosis H37Rv, Staphylococcus aureus NCTC 8325, and Klebsiella pneumoniae HS11286, and used the synthetic reads as truth sets for evaluating several popular variant callers. Insertions proved especially challenging for most variant callers to correctly identify, relative to deletions and single nucleotide polymorphisms. With adequate read depth, however, variant callers that use high quality soft-clipped reads and base mismatches to perform local realignment consistently had the highest precision and recall in identifying insertions and deletions ranging from1 to 50 bp. The remaining variant callers had lower recall values associated with identification of insertions greater than 20 bp.
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Affiliation(s)
- Yee Mey Seah
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA
| | - Mary K. Stewart
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA
| | - Daniel Hoogestraat
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA
| | - Molly Ryder
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA
| | - Brad T. Cookson
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA
| | - Noah G. Hoffman
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA
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9
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Vargas R, Luna MJ, Freschi L, Marin M, Froom R, Murphy KC, Campbell EA, Ioerger TR, Sassetti CM, Farhat MR. Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A 2023; 120:e2301394120. [PMID: 37399390 PMCID: PMC10334774 DOI: 10.1073/pnas.2301394120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/03/2023] [Indexed: 07/05/2023] Open
Abstract
Phase variation induced by insertions and deletions (INDELs) in genomic homopolymeric tracts (HT) can silence and regulate genes in pathogenic bacteria, but this process is not characterized in MTBC (Mycobacterium tuberculosis complex) adaptation. We leverage 31,428 diverse clinical isolates to identify genomic regions including phase-variants under positive selection. Of 87,651 INDEL events that emerge repeatedly across the phylogeny, 12.4% are phase-variants within HTs (0.02% of the genome by length). We estimated the in-vitro frameshift rate in a neutral HT at 100× the neutral substitution rate at [Formula: see text] frameshifts/HT/year. Using neutral evolution simulations, we identified 4,098 substitutions and 45 phase-variants to be putatively adaptive to MTBC (P < 0.002). We experimentally confirm that a putatively adaptive phase-variant alters the expression of espA, a critical mediator of ESX-1-dependent virulence. Our evidence supports the hypothesis that phase variation in the ESX-1 system of MTBC can act as a toggle between antigenicity and survival in the host.
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Affiliation(s)
- Roger Vargas
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA02115
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Michael J. Luna
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Maximillian Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY10065
| | - Kenan C. Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | | | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX77843
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Maha Reda Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA02114
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10
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Malaga W, Payros D, Meunier E, Frigui W, Sayes F, Pawlik A, Orgeur M, Berrone C, Moreau F, Mazères S, Gonzalo-Asensio J, Rengel D, Martin C, Astarie-Dequeker C, Mourey L, Brosch R, Guilhot C. Natural mutations in the sensor kinase of the PhoPR two-component regulatory system modulate virulence of ancestor-like tuberculosis bacilli. PLoS Pathog 2023; 19:e1011437. [PMID: 37450466 PMCID: PMC10348564 DOI: 10.1371/journal.ppat.1011437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/22/2023] [Indexed: 07/18/2023] Open
Abstract
The molecular factors and genetic adaptations that contributed to the emergence of Mycobacterium tuberculosis (MTB) from an environmental Mycobacterium canettii-like ancestor, remain poorly investigated. In MTB, the PhoPR two-component regulatory system controls production and secretion of proteins and lipid virulence effectors. Here, we describe that several mutations, present in phoR of M. canettii relative to MTB, impact the expression of the PhoP regulon and the pathogenicity of the strains. First, we establish a molecular model of PhoR and show that some substitutions found in PhoR of M. canettii are likely to impact the structure and activity of this protein. Second, we show that STB-K, the most attenuated available M. canettii strain, displays lower expression of PhoP-induced genes than MTB. Third, we demonstrate that genetic swapping of the phoPR allele from STB-K with the ortholog from MTB H37Rv enhances expression of PhoP-controlled functions and the capacities of the recombinant strain to colonize human macrophages, the MTB target cells, as well as to cause disease in several mouse infection models. Fourth, we extended these observations to other M. canettii strains and confirm that PhoP-controlled functions are expressed at lower levels in most M. canettii strains than in M. tuberculosis. Our findings suggest that distinct PhoR variants have been selected during the evolution of tuberculosis bacilli, contributing to higher pathogenicity and persistence of MTB in the mammalian host.
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Affiliation(s)
- Wladimir Malaga
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Delphine Payros
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Eva Meunier
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Wafa Frigui
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Fadel Sayes
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Alexandre Pawlik
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Céline Berrone
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Flavie Moreau
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Serge Mazères
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Jesus Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Facultad de Medicina, Departamento de Microbiologia, Pediatria, Radiologica y Salud Pùblica, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Institudo de Salud Carlos III, Madrid, Spain
| | - David Rengel
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Carlos Martin
- Grupo de Genética de Micobacterias, Facultad de Medicina, Departamento de Microbiologia, Pediatria, Radiologica y Salud Pùblica, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Institudo de Salud Carlos III, Madrid, Spain
- Servicio de Microbiologia, Hospital Universitario Miguel Servet, ISS Aragon, Zaragoza, Spain
| | - Catherine Astarie-Dequeker
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
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11
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Dekhil N, Mardassi H. Genomic changes underpinning the emergence of a successful Mycobacterium tuberculosis Latin American and Mediterranean clonal complex. Front Microbiol 2023; 14:1159994. [PMID: 37425998 PMCID: PMC10325029 DOI: 10.3389/fmicb.2023.1159994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/26/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction The Latin American and Mediterranean sublineage (L4.3/LAM) is the most common generalist sublineage of Mycobacterium tuberculosis lineage 4 (L4), yet certain L4.3/LAM genotypes appear to be confined to particular geographic regions. This is typically the case of a L4.3/LAM clonal complex (CC), TUN4.3_CC1, which is the most preponderant in Tunisia (61.5% of L4.3/LAM). Methods Here, we used whole-genome sequencing data of 346 globally distributed L4 clinical strains, including 278 L4.3/LAM isolates, to reconstruct the evolutionary history of TUN4.3_CC1 and delineate critical genomic changes underpinning its success. Results and Discussion Phylogenomic coupled to phylogeographic analyses indicated that TUN4.3_CC1 has evolved locally, being confined mainly to North Africa. Maximum likelihood analyses using the site and branch-site models of the PAML package disclosed strong evidence of positive selection in the gene category "cell wall and cell processes" of TUN4.3_CC1. Collectively, the data indicate that TUN4.3_CC1 has inherited several mutations, which could have potentially contributed to its evolutionary success. Of particular interest are amino acid replacements at the esxK and eccC2 genes of the ESX/Type VII secretion system, which were found to be specific to TUN4.3_CC1, being common to almost all isolates. Because of its homoplastic nature, the esxK mutation could potentially have endowed TUN4.3_CC1 with a selective advantage. Moreover, we noticed the occurrence of additional, previously described homoplasic nonsense mutations in ponA1 and Rv0197. The mutation in the latter gene, a putative oxido-reductase, has previously been shown to be correlated with enhanced transmissibility in vivo. In sum, our findings unveiled several features underpinning the success of a locally evolved L4.3/LAM clonal complex, lending further support to the critical role of genes encoded by the ESX/type VII secretion system.
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12
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López MG, Campos-Herrero MI, Torres-Puente M, Cañas F, Comín J, Copado R, Wintringer P, Iqbal Z, Lagarejos E, Moreno-Molina M, Pérez-Lago L, Pino B, Sante L, García de Viedma D, Samper S, Comas I. Deciphering the Tangible Spatio-Temporal Spread of a 25-Year Tuberculosis Outbreak Boosted by Social Determinants. Microbiol Spectr 2023; 11:e0282622. [PMID: 36786614 PMCID: PMC10100973 DOI: 10.1128/spectrum.02826-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
Outbreak strains of Mycobacterium tuberculosis are promising candidates as targets in the search for intrinsic determinants of transmissibility, as they are responsible for many cases with sustained transmission; however, the use of low-resolution typing methods and restricted geographical investigations represent flaws in assessing the success of long-lived outbreak strains. We can now address the nature of outbreak strains by combining large genomic data sets and phylodynamic approaches. We retrospectively sequenced the whole genome of representative samples assigned to an outbreak circulating in the Canary Islands (the GC strain) since 1993, which accounts for ~20% of local tuberculosis cases. We selected a panel of specific single nucleotide polymorphism (SNP) markers for an in-silico search for additional outbreak-related sequences within publicly available tuberculosis genomic data. Using this information, we inferred the origin, spread, and epidemiological parameters of the GC strain. Our approach allowed us to accurately trace the historical and more recent dispersion of the GC strain. We provide evidence of a highly successful nature within the Canarian archipelago but limited expansion abroad. Estimation of epidemiological parameters from genomic data disagree with a distinctive biology of the GC strain. With the increasing availability of genomic data allowing for the accurate inference of strain spread and critical epidemiological parameters, we can now revisit the link between Mycobacterium tuberculosis genotypes and transmission, as is routinely carried out for SARS-CoV-2 variants of concern. We demonstrate that social determinants rather than intrinsically higher bacterial transmissibility better explain the success of the GC strain. Importantly, our approach can be used to trace and characterize strains of interest worldwide. IMPORTANCE Infectious disease outbreaks represent a significant problem for public health. Tracing outbreak expansion and understanding the main factors behind emergence and persistence remain critical to effective disease control. Our study allows researchers and public health authorities to use Whole-Genome Sequencing-based methods to trace outbreaks, and shows how available epidemiological information helps to evaluate the factors underpinning outbreak persistence. Taking advantage of all the freely available information placed in public repositories, researchers can accurately establish the expansion of an outbreak beyond original boundaries, and determine the potential risk of a strain to inform health authorities which, in turn, can define target strategies to mitigate expansion and persistence. Finally, we show the need to evaluate strain transmissibility in different geographic contexts to unequivocally associate spread to local or pathogenic factors, an important lesson taken from genomic surveillance of SARS-CoV-2.
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Affiliation(s)
- Mariana G. López
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Ma Isolina Campos-Herrero
- Servicio de Microbiología, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Fernando Cañas
- Hospital Universitario Insular de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Jessica Comín
- Instituto Aragonés de Ciencias de la Salud, Fundación IIS Aragón, Zaragoza, Spain
| | - Rodolfo Copado
- Hospital José Molina Orosa, Las Palmas de Gran Canaria, Spain
| | - Penelope Wintringer
- European Molecular Biology Laboratory – European Bioinformatics Institute, Hinxton, UK
| | - Zamin Iqbal
- European Molecular Biology Laboratory – European Bioinformatics Institute, Hinxton, UK
| | - Eduardo Lagarejos
- Servicio de Microbiología, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Miguel Moreno-Molina
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Laura Pérez-Lago
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Berta Pino
- Hospital Nuestra Señora de la Candelaria, Santa Cruz de Tenerife, Spain
| | - Laura Sante
- Hospital Universitario de Canarias, Santa Cruz de Tenerife, Spain
| | - Darío García de Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Sofía Samper
- Instituto Aragonés de Ciencias de la Salud, Fundación IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
- CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
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13
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Abstract
Coughing is a dynamic physiological process resulting from input of vagal sensory neurons innervating the airways and perceived airway irritation. Although cough serves to protect and clear the airways, it can also be exploited by respiratory pathogens to facilitate disease transmission. Microbial components or infection-induced inflammatory mediators can directly interact with sensory nerve receptors to induce a cough response. Analysis of cough-generated aerosols and transmission studies have further demonstrated how infectious disease is spread through coughing. This review summarizes the neurophysiology of cough, cough induction by respiratory pathogens and inflammation, and cough-mediated disease transmission.
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Affiliation(s)
- Kubra F Naqvi
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA;
| | - Stuart B Mazzone
- Department of Anatomy and Physiology, University of Melbourne, Victoria, Australia
| | - Michael U Shiloh
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA;
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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14
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Tonkin-Hill G, Gladstone RA, Pöntinen AK, Arredondo-Alonso S, Bentley SD, Corander J. Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe. Genome Res 2023; 33:129-140. [PMID: 36669850 PMCID: PMC9977150 DOI: 10.1101/gr.277340.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 12/14/2022] [Indexed: 01/21/2023]
Abstract
Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.
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Affiliation(s)
- Gerry Tonkin-Hill
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway;,Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
| | | | - Anna K. Pöntinen
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway;,Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
| | - Stephen D. Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway;,Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom;,Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
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15
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Nimmo C, Millard J, Faulkner V, Monteserin J, Pugh H, Johnson EO. Evolution of Mycobacterium tuberculosis drug resistance in the genomic era. Front Cell Infect Microbiol 2022; 12:954074. [PMID: 36275027 PMCID: PMC9585206 DOI: 10.3389/fcimb.2022.954074] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium tuberculosis has acquired drug resistance to all drugs that have been used against it, including those only recently introduced into clinical practice. Compared to other bacteria, it has a well conserved genome due to its role as an obligate human pathogen that has adapted to a niche over five to ten thousand years. These features facilitate reconstruction and dating of M. tuberculosis phylogenies, giving key insights into how resistance has been acquired and spread globally. Resistance to each new drug has occurred within five to ten years of clinical use and has occurred even more rapidly with recently introduced drugs. In most cases, resistance-conferring mutations come with a fitness cost, but this can be overcome by compensatory mutations which restore fitness to that of wild-type bacteria. It is likely that M. tuberculosis acquires drug resistance while maintaining limited genomic variability due the generation of low frequency within-host variation, combined with ongoing purifying selection causing loss of variants without a clear fitness advantage. However, variants that do confer an advantage, such as drug resistance, can increase in prevalence amongst all bacteria within a host and become the dominant clone. These resistant strains can then be transmitted leading to primary drug resistant infection in a new host. As many countries move towards genomic methods for diagnosis of M. tuberculosis infection and drug resistance, it is important to be aware of the implications for the evolution of resistance. Currently, understanding of resistance-conferring mutations is incomplete, and some targeted genetic diagnostics create their own selective pressures. We discuss an example where a rifampicin resistance-conferring mutation which was not routinely covered by standard testing became dominant. Finally, resistance to new drugs such as bedaquiline and delamanid is caused by individually rare mutations occurring across a large mutational genomic target that have been detected over a short time, and do not provide statistical power for genotype-phenotype correlation – in contrast to longer-established drugs that form the backbone of drug-sensitive antituberculosis therapy. Therefore, we need a different approach to identify resistance-conferring mutations of new drugs before their resistance becomes widespread, abrogating their usefulness.
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Affiliation(s)
- Camus Nimmo
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
- *Correspondence: Camus Nimmo,
| | - James Millard
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Valwynne Faulkner
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Johana Monteserin
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Hannah Pugh
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Eachan Oliver Johnson
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
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16
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Soler-Camargo NC, Silva-Pereira TT, Zimpel CK, Camacho MF, Zelanis A, Aono AH, Patané JS, Dos Santos AP, Guimarães AMS. The rate and role of pseudogenes of the Mycobacterium tuberculosis complex. Microb Genom 2022; 8. [PMID: 36250787 DOI: 10.1099/mgen.0.000876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whole-genome sequence analyses have significantly contributed to the understanding of virulence and evolution of the Mycobacterium tuberculosis complex (MTBC), the causative pathogens of tuberculosis. Most MTBC evolutionary studies are focused on single nucleotide polymorphisms and deletions, but rare studies have evaluated gene content, whereas none has comprehensively evaluated pseudogenes. Accordingly, we describe an extensive study focused on quantifying and predicting possible functions of MTBC and Mycobacterium canettii pseudogenes. Using NCBI's PGAP-detected pseudogenes, we analysed 25 837 pseudogenes from 158 MTBC and M. canetii strains and combined transcriptomics and proteomics of M. tuberculosis H37Rv to gain insights about pseudogenes' expression. Our results indicate significant variability concerning rate and conservancy of in silico predicted pseudogenes among different ecotypes and lineages of tuberculous mycobacteria and pseudogenization of important virulence factors and genes of the metabolism and antimicrobial resistance/tolerance. We show that in silico predicted pseudogenes contribute considerably to MTBC genetic diversity at the population level. Moreover, the transcription machinery of M. tuberculosis can fully transcribe most pseudogenes, indicating intact promoters and recent pseudogene evolutionary emergence. Proteomics of M. tuberculosis and close evaluation of mutational lesions driving pseudogenization suggest that few in silico predicted pseudogenes are likely capable of neofunctionalization, nonsense mutation reversal, or phase variation, contradicting the classical definition of pseudogenes. Such findings indicate that genome annotation should be accompanied by proteomics and protein function assays to improve its accuracy. While indels and insertion sequences are the main drivers of the observed mutational lesions in these species, population bottlenecks and genetic drift are likely the evolutionary processes acting on pseudogenes' emergence over time. Our findings unveil a new perspective on MTBC's evolution and genetic diversity.
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Affiliation(s)
- Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Maurício F Camacho
- Functional Proteomics Laboratory, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Alexandre H Aono
- Center of Molecular Biology and Genetic Engineering, University of Campinas, Campinas, SP, Brazil.,Institute of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | | | | | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University
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17
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Dong Y, Feng Y, Ou X, Liu C, Fan W, Zhao Y, Hu Y, Zhou X. Genomic analysis of diversity, biogeography, and drug resistance in Mycobacterium bovis. Transbound Emerg Dis 2022; 69:e2769-e2778. [PMID: 35695307 DOI: 10.1111/tbed.14628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
Abstract
Mycobacterium bovis is the cause of bovine tuberculosis, and it can also cause disease in humans, with symptoms similar to those caused by Mycobacterium tuberculosis. However, our understanding of its genomic diversity, biogeography, and drug resistance remains incomplete. We performed a comparative and phylogenetic analysis of 3,228 M. bovis genomes from 24 countries. Following drug susceptibility testing, we applied a bacterial genome-wide association study to capture associations between genomic variation and drug resistance in 74 newly isolated strains from China. The data show that the cattle-adapted M. bovis were divided into six lineages with a strong phylogeographical population structure. Lineage 1 and Lineage 6 are the most widespread globally, while others show a strong geographical restriction. 17.39% of M. bovis isolates were resistant to at least one drug in China. Furthermore, we identify genomic variations associated with an increased risk of resistance acquisition. This study furthers our knowledge of M. bovis diversity, biogeography, and drug resistance and will facilitate more deeply informed genomic tracking and surveillance to minimize its threat to human health, as a cause of zoonotic tuberculosis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yuhui Dong
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Chunfa Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Weixing Fan
- National Reference Laboroatory for Animal Tuberculosis, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiangmei Zhou
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
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18
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Ceres KM, Stanhope MJ, Gröhn YT. A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation. Microb Genom 2022; 8. [PMID: 35763423 PMCID: PMC9455707 DOI: 10.1099/mgen.0.000839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The increased accessibility of next generation sequencing has allowed enough genomes from a given bacterial species to be sequenced to describe the distribution of genes in the pangenome, without limiting analyses to genes present in reference strains. Although some taxa have thousands of whole genome sequences available on public databases, most genomes were sequenced with short read technology, resulting in incomplete assemblies. Studying pangenomes could lead to important insights into adaptation, pathogenicity, or molecular epidemiology, however given the known information loss inherent in analyzing contig-level assemblies, these inferences may be biased or inaccurate. In this study we describe the pangenome of a clonally evolving pathogen,
Mycobacterium bovis
, and examine the utility of gene content variation in
M. bovis
outbreak investigation. We constructed the
M. bovis
pangenome using 1463 de novo assembled genomes. We tested the assumption of strict clonal evolution by studying evidence of recombination in core genes and analyzing the distribution of accessory genes among core monophyletic groups. To determine if gene content variation could be utilized in outbreak investigation, we carefully examined accessory genes detected in a well described
M. bovis
outbreak in Minnesota. We found significant errors in accessory gene classification. After accounting for these errors, we show that
M. bovis
has a much smaller accessory genome than previously described and provide evidence supporting ongoing clonal evolution and a closed pangenome, with little gene content variation generated over outbreaks. We also identified frameshift mutations in multiple genes, including a mutation in glpK, which has recently been associated with antibiotic tolerance in
Mycobacterium tuberculosis
. A pangenomic approach enables a more comprehensive analysis of genome dynamics than is possible with reference-based approaches; however, without critical evaluation of accessory gene content, inferences of transmission patterns employing these loci could be misguided.
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Affiliation(s)
- Kristina M Ceres
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.,Population and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.,Population and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yrjö T Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.,Population and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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19
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Sabin S, Morales-Arce AY, Pfeifer SP, Jensen JD. The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis. G3 (BETHESDA, MD.) 2022; 12:jkac055. [PMID: 35253851 PMCID: PMC9073693 DOI: 10.1093/g3journal/jkac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/28/2022] [Indexed: 12/04/2022]
Abstract
Mycobacterium canettii is a causative agent of tuberculosis in humans, along with the members of the Mycobacterium tuberculosis complex. Frequently used as an outgroup to the M. tuberculosis complex in phylogenetic analyses, M. canettii is thought to offer the best proxy for the progenitor species that gave rise to the complex. Here, we leverage whole-genome sequencing data and biologically relevant population genomic models to compare the evolutionary dynamics driving variation in the recombining M. canettii with that in the nonrecombining M. tuberculosis complex, and discuss differences in observed genomic diversity in the light of expected levels of Hill-Robertson interference. In doing so, we highlight the methodological challenges of estimating recombination rates through traditional population genetic approaches using sequences called from populations of microorganisms and evaluate the likely mis-inference that arises owing to a neglect of common model violations including purifying selection, background selection, progeny skew, and population size change. In addition, we compare performance when full within-host polymorphism data are utilized, versus the more common approach of basing analyses on within-host consensus sequences.
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Affiliation(s)
- Susanna Sabin
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Ana Y Morales-Arce
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Susanne P Pfeifer
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
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20
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Gene evolutionary trajectories in Mycobacterium tuberculosis reveal temporal signs of selection. Proc Natl Acad Sci U S A 2022; 119:e2113600119. [PMID: 35452305 PMCID: PMC9173582 DOI: 10.1073/pnas.2113600119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
SignificancePrevious attempts to identify the action of natural selection in the Mycobacterium tuberculosis complex (MTBC) were limited by sample size and averaging across time and lineages. We investigate changes in selective pressures across time for every single gene of the MTBC. We developed a methodology to analyze temporal signals of selection in a large dataset (∼5,000 complete genomes) and showed that 1) almost half of the genes seem to have been under positive selection at some point in time; 2) experimentally confirmed epitopes tend to accumulate more mutations in deeper branches than in external branches; and 3) temporal signals identify genes that were conserved in the past but under positive selection in the present, suggesting ongoing adaptation to the host.
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21
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Sacristán C, Costa-Silva S, Reisfeld L, Navas-Suárez PE, Ewbank AC, Duarte-Benvenuto A, Coelho Couto de Azevedo Fernandes N, Albergaria Ressio R, Antonelli M, Rocha Lorenço J, Favero CM, Marigo J, Kolesnikovas CKM, Catão-Dias JL. Novel alphaherpesvirus in a wild South American sea lion (Otaria byronia) with pulmonary tuberculosis. Braz J Microbiol 2021; 52:2489-2498. [PMID: 34580836 PMCID: PMC8578510 DOI: 10.1007/s42770-021-00614-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/19/2021] [Indexed: 11/28/2022] Open
Abstract
In 2017, an adult male South American sea lion (Otaria byronia), presenting emaciation and a cervical abscess, stranded alive in Florianópolis, southern Brazil. The animal was directed to a rehabilitation center, dying a few days later. On necropsy, the main gross findings were necrotizing lymphadenitis of the right prescapular lymph node and nodular bronchopneumonia. A novel alphaherpesvirus, tentatively named Otariid alphaherpesvirus 1, was amplified in several tissue samples. No histopathologic findings associated with viral infection were observed. Additionally, pulmonary tuberculosis by Mycobacterium pinnipedii was diagnosed by histopathological, immunohistochemical, and molecular techniques. Several bacteria were cultured from antemortem and postmortem samples, including Proteus mirabilis from the cervical abscess and cardiac blood, and Escherichia coli from the cervical abscess and pericardial effusion. Flavivirus, morbillivirus, and Apicomplexa were not detected by molecular techniques. Herein, we report a novel alphaherpesvirus in a pinniped species of the family Otariidae. Although previously described in Southern Hemisphere pinniped species, including South American sea lions, there is limited information regarding M. pinnipedii impact over this group. Further research is required to determine the associated pathogenesis of this novel herpesvirus, and prevalence of Otariid alphaherpesvirus 1 and M. pinnipedii in the reproductive colonies.
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Affiliation(s)
- Carlos Sacristán
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil.
| | - Samira Costa-Silva
- Associação R3 Animal, Florianópolis, SC, 88061-500, Brazil
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | | | - Pedro Enrique Navas-Suárez
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | - Ana Carolina Ewbank
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | - Aricia Duarte-Benvenuto
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | - Natália Coelho Couto de Azevedo Fernandes
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
- Centro de Patologia, Instituto Adolfo Lutz, São Paulo, SP, 01246000, Brazil
| | | | | | | | - Cíntia Maria Favero
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | - Juliana Marigo
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
| | | | - José Luiz Catão-Dias
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, 05508-270, Brazil
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22
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Pla-Díaz M, Sánchez-Busó L, Giacani L, Šmajs D, Bosshard PP, Bagheri HC, Schuenemann VJ, Nieselt K, Arora N, González-Candelas F. Evolutionary processes in the emergence and recent spread of the syphilis agent, Treponema pallidum. Mol Biol Evol 2021; 39:6427636. [PMID: 34791386 PMCID: PMC8789261 DOI: 10.1093/molbev/msab318] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.
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Affiliation(s)
- Marta Pla-Díaz
- Unidad Mixta Infección y Salud Pública FISABIO/Universidad de Valencia-I2SysBio, Spain.,CIBER in Epidemiology and Public Health, Spain
| | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, and Department of Global Health, University of Washington, Seattle, WA, USA
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Czech Republic
| | - Philipp P Bosshard
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | | | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Germany
| | - Natasha Arora
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland.,Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO/Universidad de Valencia-I2SysBio, Spain.,CIBER in Epidemiology and Public Health, Spain.,Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain
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23
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Freschi L, Vargas R, Husain A, Kamal SMM, Skrahina A, Tahseen S, Ismail N, Barbova A, Niemann S, Cirillo DM, Dean AS, Zignol M, Farhat MR. Population structure, biogeography and transmissibility of Mycobacterium tuberculosis. Nat Commun 2021; 12:6099. [PMID: 34671035 PMCID: PMC8528816 DOI: 10.1038/s41467-021-26248-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 09/06/2021] [Indexed: 01/10/2023] Open
Abstract
Mycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity and biogeography remains incomplete. Here we use a combination of phylogenetics and dimensionality reduction to reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4. We assess sub-lineages using genomic sequences from 4939 pan-susceptible strains, and find 30 new genetically distinct clades that we validate in a dataset of 4645 independent isolates. We find a consistent geographically restricted or unrestricted pattern for 20 groups, including three groups of Lineage 1. The distribution of terminal branch lengths across the M. tuberculosis phylogeny supports the hypothesis of a higher transmissibility of Lineages 2 and 4, in comparison with Lineages 3 and 1, on a global scale. We define an expanded barcode of 95 single nucleotide substitutions that allows rapid identification of 69 M. tuberculosis sub-lineages and 26 additional internal groups. Our results paint a higher resolution picture of the M. tuberculosis phylogeny and biogeography.
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Affiliation(s)
- Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ashaque Husain
- Directorate General of Health Services, Ministry of Health and Family Welfare, Dhaka, Bangladesh
| | - S M Mostofa Kamal
- Department of Pathology and Microbiology, National Institute of Diseases of the Chest and Hospital, Dhaka, Bangladesh
| | - Alena Skrahina
- Republican Scientific and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Sabira Tahseen
- National Reference Laboratory, National Tuberculosis Control Programme, Islamabad, Pakistan
| | - Nazir Ismail
- National Institute for Communicable Diseases, Sandringham, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anna Barbova
- Central Reference Laboratory on Tuberculosis Microbiological Diagnostics, Ministry of Health, Kiev, Ukraine
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Borstel Research Centre, Borstel, Germany
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anna S Dean
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Matteo Zignol
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Maha Reda Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA.
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24
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Reis AC, Cunha MV. Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis. Sci Rep 2021; 11:18789. [PMID: 34552144 PMCID: PMC8458382 DOI: 10.1038/s41598-021-98226-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/27/2021] [Indexed: 02/08/2023] Open
Abstract
Genome sequencing has reinvigorated the infectious disease research field, shedding light on disease epidemiology, pathogenesis, host-pathogen interactions and also evolutionary processes exerted upon pathogens. Mycobacterium tuberculosis complex (MTBC), enclosing M. bovis as one of its animal-adapted members causing tuberculosis (TB) in terrestrial mammals, is a paradigmatic model of bacterial evolution. As other MTBC members, M. bovis is postulated as a strictly clonal, slowly evolving pathogen, with apparently no signs of recombination or horizontal gene transfer. In this work, we applied comparative genomics to a whole genome sequence (WGS) dataset composed by 70 M. bovis from different lineages (European and African) to gain insights into the evolutionary forces that shape genetic diversification in M. bovis. Three distinct approaches were used to estimate signs of recombination. Globally, a small number of recombinant events was identified and confirmed by two independent methods with solid support. Still, recombination reveals a weaker effect on M. bovis diversity compared with mutation (overall r/m = 0.037). The differential r/m average values obtained across the clonal complexes of M. bovis in our dataset are consistent with the general notion that the extent of recombination may vary widely among lineages assigned to the same taxonomical species. Based on this work, recombination in M. bovis cannot be excluded and should thus be a topic of further effort in future comparative genomics studies for which WGS of large datasets from different epidemiological scenarios across the world is crucial. A smaller M. bovis dataset (n = 42) from a multi-host TB endemic scenario was then subjected to additional analyses, with the identification of more than 1,800 sites wherein at least one strain showed a single nucleotide polymorphism (SNP). The majority (87.1%) was located in coding regions, with the global ratio of non-synonymous upon synonymous alterations (dN/dS) exceeding 1.5, suggesting that positive selection is an important evolutionary force exerted upon M. bovis. A higher percentage of SNPs was detected in genes enriched into "lipid metabolism", "cell wall and cell processes" and "intermediary metabolism and respiration" functional categories, revealing their underlying importance in M. bovis biology and evolution. A closer look on genes prone to horizontal gene transfer in the MTBC ancestor and included in the 3R (DNA repair, replication and recombination) system revealed a global average negative value for Taijima's D neutrality test, suggesting that past selective sweeps and population expansion after a recent bottleneck remain as major evolutionary drivers of the obligatory pathogen M. bovis in its struggle with the host.
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Affiliation(s)
- Ana C Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Room 2.4.11, 1749-016, Lisbon, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Room 2.4.11, 1749-016, Lisbon, Portugal.
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.
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25
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Castro RAD, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 45:fuaa071. [PMID: 33320947 PMCID: PMC8371278 DOI: 10.1093/femsre/fuaa071] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The etiological agents of human TB are a closely-related group of human-adapted bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Understanding how MTBC populations evolve within-host may allow for improved TB treatment and control strategies. In this review, we highlight recent works that have shed light on how AMR evolves in MTBC populations within individual patients. We discuss the role of heteroresistance in AMR evolution, and review the bacterial, patient and environmental factors that likely modulate the magnitude of heteroresistance within-host. We further highlight recent works on the dynamics of MTBC genetic diversity within-host, and discuss how spatial substructures in patients' lungs, spatiotemporal heterogeneity in antimicrobial concentrations and phenotypic drug tolerance likely modulates the dynamics of MTBC genetic diversity in patients during treatment. We note the general characteristics that are shared between how the MTBC and other bacterial pathogens evolve in humans, and highlight the characteristics unique to the MTBC.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
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26
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Parallel in vivo experimental evolution reveals that increased stress resistance was key for the emergence of persistent tuberculosis bacilli. Nat Microbiol 2021; 6:1082-1093. [PMID: 34294904 DOI: 10.1038/s41564-021-00938-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 06/18/2021] [Indexed: 12/31/2022]
Abstract
Pathogenomic evidence suggests that Mycobacterium tuberculosis (MTB) evolved from an environmental ancestor similar to Mycobacterium canettii, a rare human pathogen. Although the adaptations responsible for this transition are poorly characterized, the ability to persist in humans seems to be important. We set out to identify the adaptations contributing to the evolution of persistence in MTB. We performed an experimental evolution of eight M. canettii populations in mice; four populations were derived from the isolate STB-K (phylogenomically furthest from MTB) and four from STB-D (closest to MTB), which were monitored for 15 and 6 cycles, respectively. We selected M. canettii mutants with enhanced persistence in vivo compared with the parental strains, which were phenotypically closer to MTB. Genome sequencing of 140 mutants and complementation analysis revealed that mutations in two loci were responsible for enhanced persistence. Most of the tested mutants were more resistant than their parental strains to nitric oxide, an important effector of immunity. Modern MTB were similarly more resistant to nitric oxide than M. canettii. Our findings demonstrate phenotypic convergence during experimental evolution of M. canettii, which mirrors natural evolution of MTB. Furthermore, they indicate that the ability to withstand host-induced stresses was key for the emergence of persistent MTB.
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27
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Sanoussi CN, Coscolla M, Ofori-Anyinam B, Otchere ID, Antonio M, Niemann S, Parkhill J, Harris S, Yeboah-Manu D, Gagneux S, Rigouts L, Affolabi D, de Jong BC, Meehan CJ. Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv. Microb Genom 2021; 7:000437. [PMID: 34241588 PMCID: PMC8477398 DOI: 10.1099/mgen.0.000437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/22/2021] [Indexed: 12/27/2022] Open
Abstract
Pathogens of the Mycobacterium tuberculosis complex (MTBC) are considered to be monomorphic, with little gene content variation between strains. Nevertheless, several genotypic and phenotypic factors separate strains of the different MTBC lineages (L), especially L5 and L6 (traditionally termed Mycobacterium africanum) strains, from each other. However, this genome variability and gene content, especially of L5 strains, has not been fully explored and may be important for pathobiology and current approaches for genomic analysis of MTBC strains, including transmission studies. By comparing the genomes of 355 L5 clinical strains (including 3 complete genomes and 352 Illumina whole-genome sequenced isolates) to each other and to H37Rv, we identified multiple genes that were differentially present or absent between H37Rv and L5 strains. Additionally, considerable gene content variability was found across L5 strains, including a split in the L5.3 sub-lineage into L5.3.1 and L5.3.2. These gene content differences had a small knock-on effect on transmission cluster estimation, with clustering rates influenced by the selected reference genome, and with potential overestimation of recent transmission when using H37Rv as the reference genome. We conclude that full capture of the gene diversity, especially high-resolution outbreak analysis, requires a variation of the single H37Rv-centric reference genome mapping approach currently used in most whole-genome sequencing data analysis pipelines. Moreover, the high within-lineage gene content variability suggests that the pan-genome of M. tuberculosis is at least several kilobases larger than previously thought, implying that a concatenated or reference-free genome assembly (de novo) approach may be needed for particular questions.
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Affiliation(s)
- C. N'Dira Sanoussi
- Laboratoire de Référence des Mycobactéries, Cotonou, Benin
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mireia Coscolla
- I2SysBio, University of Valencia-FISABIO Joint Unit, Valencia, Spain
| | - Boatema Ofori-Anyinam
- Food and Drugs Authority, Accra, Ghana
- Rutgers New Jersey Medical School, Rutgers University, New Jersey, USA
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Martin Antonio
- Medical Research Council Unit in The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Stefan Niemann
- German Center for Infection Research, partner site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Research Center Borstel, Molecular and Experimental Mycobacteriology, Borstel, Germany
| | - Julian Parkhill
- Wellcome Sanger Institute, Hinxton, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Bouke C. de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
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Gabbassov E, Moreno-Molina M, Comas I, Libbrecht M, Chindelevitch L. SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data. Microb Genom 2021; 7. [PMID: 34165419 PMCID: PMC8461467 DOI: 10.1099/mgen.0.000607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The occurrence of multiple strains of a bacterial pathogen such as M. tuberculosis or C. difficile within a single human host, referred to as a mixed infection, has important implications for both healthcare and public health. However, methods for detecting it, and especially determining the proportion and identities of the underlying strains, from WGS (whole-genome sequencing) data, have been limited. In this paper we introduce SplitStrains, a novel method for addressing these challenges. Grounded in a rigorous statistical model, SplitStrains not only demonstrates superior performance in proportion estimation to other existing methods on both simulated as well as real M. tuberculosis data, but also successfully determines the identity of the underlying strains. We conclude that SplitStrains is a powerful addition to the existing toolkit of analytical methods for data coming from bacterial pathogens and holds the promise of enabling previously inaccessible conclusions to be drawn in the realm of public health microbiology.
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Affiliation(s)
- Einar Gabbassov
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
- *Correspondence: Einar Gabbassov,
| | | | - Iñaki Comas
- Instituto de Biomedicina de Valencia, Valencia, Spain
| | - Maxwell Libbrecht
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Leonid Chindelevitch
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College, London, UK
- *Correspondence: Leonid Chindelevitch,
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29
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Menardo F, Gagneux S, Freund F. Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis. Mol Biol Evol 2021; 38:290-306. [PMID: 32667991 PMCID: PMC8480183 DOI: 10.1093/molbev/msaa179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Kingman coalescent and its developments are often considered among the most important advances in population genetics of the last decades. Demographic inference based on coalescent theory has been used to reconstruct the population dynamics and evolutionary history of several species, including Mycobacterium tuberculosis (MTB), an important human pathogen causing tuberculosis. One key assumption of the Kingman coalescent is that the number of descendants of different individuals does not vary strongly, and violating this assumption could lead to severe biases caused by model misspecification. Individual lineages of MTB are expected to vary strongly in reproductive success because 1) MTB is potentially under constant selection due to the pressure of the host immune system and of antibiotic treatment, 2) MTB undergoes repeated population bottlenecks when it transmits from one host to the next, and 3) some hosts show much higher transmission rates compared with the average (superspreaders). Here, we used an approximate Bayesian computation approach to test whether multiple-merger coalescents (MMC), a class of models that allow for large variation in reproductive success among lineages, are more appropriate models to study MTB populations. We considered 11 publicly available whole-genome sequence data sets sampled from local MTB populations and outbreaks and found that MMC had a better fit compared with the Kingman coalescent for 10 of the 11 data sets. These results indicate that the null model for analyzing MTB outbreaks should be reassessed and that past findings based on the Kingman coalescent need to be revisited.
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Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sébastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabian Freund
- Department of Plant Biodiversity and Breeding Informatics, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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Abstract
Current models of horizontal gene transfer (HGT) in mycobacteria are based on “distributive conjugal transfer” (DCT), an HGT type described in the fast-growing, saprophytic model organism Mycobacterium smegmatis, which creates genome mosaicism in resulting strains and depends on an ESX-1 type VII secretion system. In contrast, only few data on interstrain DNA transfer are available for tuberculosis-causing mycobacteria, for which chromosomal DNA transfer between two Mycobacterium canettii strains was reported, a process which, however, was not observed for Mycobacterium tuberculosis strains. Here, we have studied a wide range of human- and animal-adapted members of the Mycobacterium tuberculosis complex (MTBC) using an optimized filter-based mating assay together with three selected strains of M. canettii that acted as DNA recipients. Unlike in previous approaches, we obtained a high yield of thousands of recombinants containing transferred chromosomal DNA fragments from various MTBC donor strains, as confirmed by whole-genome sequence analysis of 38 randomly selected clones. While the genome organizations of the obtained recombinants showed mosaicisms of donor DNA fragments randomly integrated into a recipient genome backbone, reminiscent of those described as being the result of ESX-1-mediated DCT in M. smegmatis, we observed similar transfer efficiencies when ESX-1-deficient donor and/or recipient mutants were used, arguing that in tubercle bacilli, HGT is an ESX-1-independent process. These findings provide new insights into the genetic events driving the pathoevolution of M. tuberculosis and radically change our perception of HGT in mycobacteria, particularly for those species that show recombinogenic population structures despite the natural absence of ESX-1 secretion systems.
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31
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Zakham F, Sironen T, Vapalahti O, Kant R. Pan and Core Genome Analysis of 183 Mycobacterium tuberculosis Strains Revealed a High Inter-Species Diversity among the Human Adapted Strains. Antibiotics (Basel) 2021; 10:antibiotics10050500. [PMID: 33924811 PMCID: PMC8145561 DOI: 10.3390/antibiotics10050500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/24/2021] [Accepted: 04/25/2021] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) is an airborne communicable disease with high morbidity and mortality rates, especially in developing countries. The causal agents of TB belong to the complex Mycobacterium tuberculosis (MTBc), which is composed of different human and animal TB associated species. Some animal associated species have zoonotic potential and add to the burden of TB management. The BCG ("Bacillus Calmette-Guérin") vaccine is widely used for the prevention against TB, but its use is limited in immunocompromised patients and animals due to the adverse effects and disseminated life-threatening complications. In this study, we aimed to carry out a comparative genome analysis between the human adapted species including BCG vaccine strains to identify and pinpoint the conserved genes related to the virulence across all the species, which could add a new value for vaccine development. For this purpose, the sequences of 183 Mycobacterium tuberculosis (MTB) strains were retrieved from the freely available WGS dataset at NCBI. The species included: 168 sensu stricto MTB species with other human MTB complex associated strains: M. tuberculosis var. africanum (3), M. tuberculosis var. bovis (2 draft genomes) and 10 BCG species, which enabled the analysis of core genome which contains the conserved genes and some virulence factor determinants. Further, a phylogenetic tree was constructed including the genomes of human (183); animals MTB adapted strains (6) and the environmental Mycobacterium strain "M. canettii". Our results showed that the core genome consists of 1166 conserved genes among these species, which represents a small portion of the pangenome (7036 genes). The remaining genes in the pangenome (5870) are accessory genes, adding a high inter-species diversity. Further, the core genome includes several virulence-associated genes and this could explain the rare infectiousness potential of some attenuated vaccine strains in some patients. This study reveals that low number of conserved genes in human adapted MTBc species and high inter-species diversity of the pan-genome could be considered for vaccine candidate development.
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Affiliation(s)
- Fathiah Zakham
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (F.Z.); (T.S.); (O.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
- Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (F.Z.); (T.S.); (O.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (F.Z.); (T.S.); (O.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
- HUSLAB, Hospital District of Helsinki and Uusimaa, 00260 Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (F.Z.); (T.S.); (O.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
- Correspondence:
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32
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Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau. Proc Natl Acad Sci U S A 2021; 118:2017831118. [PMID: 33879609 DOI: 10.1073/pnas.2017831118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During its global dispersal, Mycobacterium tuberculosis (Mtb) has encountered varied geographic environments and host populations. Although local adaptation seems to be a plausible model for describing long-term host-pathogen interactions, genetic evidence for this model is lacking. Here, we analyzed 576 whole-genome sequences of Mtb strains sampled from different regions of high-altitude Tibet. Our results show that, after sequential introduction of a few ancestral strains, the Tibetan Mtb population diversified locally while maintaining strict separation from the Mtb populations on the lower altitude plain regions of China. The current population structure and estimated past population dynamics suggest that the modern Beijing sublineage strains, which expanded over most of China and other global regions, did not show an expansion advantage in Tibet. The mutations in the Tibetan strains showed a higher proportion of A > G/T > C transitions than strains from the plain regions, and genes encoding DNA repair enzymes showed evidence of positive selection. Moreover, the long-term Tibetan exclusive selection for truncating mutations in the thiol-oxidoreductase encoding sseA gene suggests that Mtb was subjected to local selective pressures associated with oxidative stress. Collectively, the population genomics of Mtb strains in the relatively isolated population of Tibet provides genetic evidence that Mtb has adapted to local environments.
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Kanabalan RD, Lee LJ, Lee TY, Chong PP, Hassan L, Ismail R, Chin VK. Human tuberculosis and Mycobacterium tuberculosis complex: A review on genetic diversity, pathogenesis and omics approaches in host biomarkers discovery. Microbiol Res 2021; 246:126674. [PMID: 33549960 DOI: 10.1016/j.micres.2020.126674] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis complex (MTBC) refers to a group of mycobacteria encompassing nine members of closely related species that causes tuberculosis in animals and humans. Among the nine members, Mycobacterium tuberculosis (M. tuberculosis) remains the main causative agent for human tuberculosis that results in high mortality and morbidity globally. In general, MTBC species are low in diversity but exhibit distinctive biological differences and phenotypes among different MTBC lineages. MTBC species are likely to have evolved from a common ancestor through insertions/deletions processes resulting in species speciation with different degrees of pathogenicity. The pathogenesis of human tuberculosis is complex and remains poorly understood. It involves multi-interactions or evolutionary co-options between host factors and bacterial determinants for survival of the MTBC. Granuloma formation as a protection or survival mechanism in hosts by MTBC remains controversial. Additionally, MTBC species are capable of modulating host immune response and have adopted several mechanisms to evade from host immune attack in order to survive in humans. On the other hand, current diagnostic tools for human tuberculosis are inadequate and have several shortcomings. Numerous studies have suggested the potential of host biomarkers in early diagnosis of tuberculosis, in disease differentiation and in treatment monitoring. "Multi-omics" approaches provide holistic views to dissect the association of MTBC species with humans and offer great advantages in host biomarkers discovery. Thus, in this review, we seek to understand how the genetic variations in MTBC lead to species speciation with different pathogenicity. Furthermore, we also discuss how the host and bacterial players contribute to the pathogenesis of human tuberculosis. Lastly, we provide an overview of the journey of "omics" approaches in host biomarkers discovery in human tuberculosis and provide some interesting insights on the challenges and directions of "omics" approaches in host biomarkers innovation and clinical implementation.
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Affiliation(s)
- Renuga Devi Kanabalan
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia
| | - Le Jie Lee
- Prima Nexus Sdn. Bhd., Menara CIMB, Jalan Stesen Sentral 2, Kuala Lumpur, Malaysia
| | - Tze Yan Lee
- Perdana University School of Liberal Arts, Science and Technology (PUScLST), Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan Damansara Heights, Kuala Lumpur, 50490, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University Lakeside Campus, Subang Jaya, 47500, Malaysia
| | - Latiffah Hassan
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia
| | - Rosnah Ismail
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia.
| | - Voon Kin Chin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia; Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Puncak Alam Campus, Bandar Puncak Alam, Selangor, 42300, Malaysia.
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34
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Comparative Genomic Analysis of Mycobacteriaceae Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis Complex. mSystems 2021; 6:6/1/e00934-20. [PMID: 33468705 PMCID: PMC7820667 DOI: 10.1128/msystems.00934-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are conserved genetic elements in many prokaryotes, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Although knowledge of CRISPR locus variability has been utilized in M. tuberculosis strain genotyping, its evolutionary path in Mycobacteriaceae is not well understood. In this study, we have performed a comparative analysis of 141 mycobacterial genomes and identified the exclusive presence of the CRISPR-Cas type III-A system in M. tuberculosis complex (MTBC). Our global phylogenetic analysis of CRISPR repeats and Cas10 proteins offers evidence of horizontal gene transfer (HGT) of the CRISPR-Cas module in the last common ancestor of MTBC and Mycobacterium canettii from a Streptococcus-like environmental bacterium. Additionally, our results show that the variation of CRISPR-Cas organization in M. tuberculosis lineages, especially in the Beijing sublineage of lineage 2, is due to the transposition of insertion sequence IS6110 The direct repeat (DR) region of the CRISPR-Cas locus acts as a hot spot for IS6110 insertion. We show in M. tuberculosis H37Rv that the repeat at the 5' end of CRISPR1 of the forward strand is an atypical repeat made up partly of IS-terminal inverted repeat and partly CRISPR DR. By tracing an undetectable spacer sequence in the DR region, the two CRISPR loci could theoretically be joined to reconstruct the ancestral single CRISPR-Cas locus organization, as seen in M. canettii This study retracing the evolutionary events of HGT and IS6110-driven genomic deletions helps us to better understand the strain-specific variations in M. tuberculosis lineages.IMPORTANCE Comparative genomic analysis of prokaryotes has led to a better understanding of the biology of several pathogenic microorganisms. One such clinically important pathogen is M. tuberculosis, the leading cause of bacterial infection worldwide. Recent evidence on the functionality of the CRISPR-Cas system in M. tuberculosis has brought back focus on these conserved genetic elements, present in many prokaryotes. Our study advances understanding of mycobacterial CRISPR-Cas origin and its diversity among the different species. We provide phylogenetic evidence of acquisition of CRISPR-Cas type III-A in the last common ancestor shared between MTBC and M. canettii, by HGT-mediated events. The most likely source of HGT was an environmental Firmicutes bacterium. Genomic mapping of the CRISPR loci showed the IS6110 transposition-driven variations in M. tuberculosis strains. Thus, this study offers insights into events related to the evolution of CRISPR-Cas in M. tuberculosis lineages.
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Santos-Pereira A, Magalhães C, Araújo PMM, Osório NS. Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: "The Tortoise and the Hare". Microorganisms 2021; 9:147. [PMID: 33440808 PMCID: PMC7827287 DOI: 10.3390/microorganisms9010147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/24/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral "mutant cloud" is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.
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Affiliation(s)
- Ana Santos-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Pedro M. M. Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
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36
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Skhairia MA, Dekhil N, Mhenni B, Fradj SB, Mardassi H. Successful expansion of Mycobacterium tuberculosis Latin American and Mediterranean sublineage (L4.3/LAM) in Tunisia mainly driven by a single, long-established clonal complex. Int J Infect Dis 2020; 103:220-225. [PMID: 33307222 DOI: 10.1016/j.ijid.2020.11.195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES To explore the evolutionary history of Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage in Tunisia, where it predominates. METHODS High-resolution genotyping of 252 L4.3/LAM clinical strains was undertaken, and whole-genome sequencing was performed on 31 representative isolates. RESULTS Genotyping data coupled with Bayesian analyses split the Tunisian L4.3/LAM strain collection into two divergent entities (65.07% vs 34.92%): a major subpopulation, dominated by a single clonal complex (CC), TUN4.3_CC1 (94.51%); and a minor subpopulation, dominated by TUN4.3_CC2 (42.04%). TUN4.3_CC1 is clearly thriving in Tunisia, accounting for 61.5% of the L4.3/LAM sublineage. TUN4.3_CC1 displayed higher mean allelic richness compared with TUN4.3_CC2 and predominated throughout the entire region, indicating a long-established history. The very low proportion of drug resistance among TUN4.3_CC1 isolates is indicative of their intrinsic ability to spread successfully in the host population. Genomic analyses further confirmed the clear genetic separation between the two main CCs (pairwise fixation index 0.56), and suggested the relatively ancient origin of TUN4.3_CC1. Consistent with its successful expansion, TUN4.3_CC1 showed reduced mean pairwise genetic distance between genomes. CONCLUSIONS These findings link the successful expansion of L4.3/LAM in Tunisia to a single long-established clone.
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Affiliation(s)
- Mohamed Amine Skhairia
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Naira Dekhil
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Besma Mhenni
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Saloua Ben Fradj
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Helmi Mardassi
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.
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37
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Morales-Arce AY, Sabin SJ, Stone AC, Jensen JD. The population genomics of within-host Mycobacterium tuberculosis. Heredity (Edinb) 2020; 126:1-9. [PMID: 33060846 DOI: 10.1038/s41437-020-00377-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 11/09/2022] Open
Abstract
Recent progress in genomic sequencing from patient samples has allowed for the first detailed insight into the within-host genetic diversity of Mycobacterium tuberculosis (M.TB), revealing remarkably low levels of variation. While this has often been attributed to low mutation rates, other factors have been described, including resistance evolution (i.e., selective sweeps), widespread purifying and background selection, and, more recently, progeny skew. Here we review recent findings pertaining to the processes governing the evolutionary dynamics of M.TB, discuss their implications for improving our understanding of this important human pathogen, and make recommendations for future work. Significantly, this emerging evolutionary framework involving the joint estimation of demographic, selective, and reproductive processes is forming a new paradigm for the study of within-host pathogen evolution that will be widely applicable across organisms.
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Affiliation(s)
- Ana Y Morales-Arce
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
| | - Susanna J Sabin
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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38
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Rivera I, Linz B, Harvill ET. Evolution and Conservation of Bordetella Intracellular Survival in Eukaryotic Host Cells. Front Microbiol 2020; 11:557819. [PMID: 33178148 PMCID: PMC7593398 DOI: 10.3389/fmicb.2020.557819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/28/2020] [Indexed: 11/25/2022] Open
Abstract
The classical bordetellae possess several partially characterized virulence mechanisms that are studied in the context of a complete extracellular life cycle in their mammalian hosts. Yet, classical bordetellae have repeatedly been reported within dendritic cells (DCs) and alveolar macrophages in clinical samples, and in vitro experiments convincingly demonstrate that the bacteria can survive intracellularly within mammalian phagocytic cells, an ability that appears to have descended from ancestral progenitor species that lived in the environment and acquired the mechanisms to resist unicellular phagocytic predators. Many pathogens, including Mycobacterium tuberculosis, Salmonella enterica, Francisella tularensis, and Legionella pneumophila, are known to parasitize and multiply inside eukaryotic host cells. This strategy provides protection, nutrients, and the ability to disseminate systemically. While some work has been dedicated at characterizing intracellular survival of Bordetella pertussis, there is limited understanding of how this strategy has evolved within the genus Bordetella and the contributions of this ability to bacterial pathogenicity, evasion of host immunity as well as within and between-host dissemination. Here, we explore the mechanisms that control the metabolic changes accompanying intracellular survival and how these have been acquired and conserved throughout the evolutionary history of the Bordetella genus and discuss the possible implications of this strategy in the persistence and reemergence of B. pertussis in recent years.
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Affiliation(s)
- Israel Rivera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Bodo Linz
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Division of Microbiology, Department of Biology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Eric T Harvill
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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39
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Peters JS, Ismail N, Dippenaar A, Ma S, Sherman DR, Warren RM, Kana BD. Genetic Diversity in Mycobacterium tuberculosis Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease. Annu Rev Genet 2020; 54:511-537. [PMID: 32926793 DOI: 10.1146/annurev-genet-022820-085940] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tuberculosis claims more human lives than any other bacterial infectious disease and represents a clear and present danger to global health as new tools for vaccination, treatment, and interruption of transmission have been slow to emerge. Additionally, tuberculosis presents with notable clinical heterogeneity, which complicates diagnosis, treatment, and the establishment of nonrelapsing cure. How this heterogeneity is driven by the diversity ofclinical isolates of the causative agent, Mycobacterium tuberculosis, has recently garnered attention. Herein, we review advances in the understanding of how naturally occurring variation in clinical isolates affects transmissibility, pathogenesis, immune modulation, and drug resistance. We also summarize how specific changes in transcriptional responses can modulate infection or disease outcome, together with strain-specific effects on gene essentiality. Further understanding of how this diversity of M. tuberculosis isolates affects disease and treatment outcomes will enable the development of more effective therapeutic options and vaccines for this dreaded disease.
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Affiliation(s)
- Julian S Peters
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
| | - Nabila Ismail
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; ,
| | - Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; , .,Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, 2000, Belgium;
| | - Shuyi Ma
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - David R Sherman
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - Robin M Warren
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; ,
| | - Bavesh D Kana
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
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Anani H, Zgheib R, Hasni I, Raoult D, Fournier PE. Interest of bacterial pangenome analyses in clinical microbiology. Microb Pathog 2020; 149:104275. [PMID: 32562810 DOI: 10.1016/j.micpath.2020.104275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.
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Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Rita Zgheib
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Issam Hasni
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
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41
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A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun 2020; 11:2917. [PMID: 32518235 PMCID: PMC7283319 DOI: 10.1038/s41467-020-16626-6] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/13/2020] [Indexed: 02/03/2023] Open
Abstract
The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to have expanded from a common progenitor in Africa. However, the molecular events that accompanied this emergence remain largely unknown. Here, we describe two MTBC strains isolated from patients with multidrug resistant tuberculosis, representing an as-yet-unknown lineage, named Lineage 8 (L8), seemingly restricted to the African Great Lakes region. Using genome-based phylogenetic reconstruction, we show that L8 is a sister clade to the known MTBC lineages. Comparison with other complete mycobacterial genomes indicate that the divergence of L8 preceded the loss of the cobF genome region - involved in the cobalamin/vitamin B12 synthesis - and gene interruptions in a subsequent common ancestor shared by all other known MTBC lineages. This discovery further supports an East African origin for the MTBC and provides additional molecular clues on the ancestral genome reduction associated with adaptation to a pathogenic lifestyle. The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to be evolved from a common progenitor in Africa. Here, the authors identify two MTBC strains isolated from patients with multidrug-resistant tuberculosis, representing an as-yet-unknown lineage further supporting an East African origin for the MTBC.
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Sousa J, Cá B, Maceiras AR, Simões-Costa L, Fonseca KL, Fernandes AI, Ramos A, Carvalho T, Barros L, Magalhães C, Chiner-Oms Á, Machado H, Veiga MI, Singh A, Pereira R, Amorim A, Vieira J, Vieira CP, Bhatt A, Rodrigues F, Rodrigues PNS, Gagneux S, Castro AG, Guimarães JT, Bastos HN, Osório NS, Comas I, Saraiva M. Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production. Nat Commun 2020; 11:1949. [PMID: 32327653 PMCID: PMC7181847 DOI: 10.1038/s41467-020-15832-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/23/2020] [Indexed: 01/26/2023] Open
Abstract
Genetic diversity of Mycobacterium tuberculosis affects immune responses and clinical outcomes of tuberculosis (TB). However, how bacterial diversity orchestrates immune responses to direct distinct TB severities is unknown. Here we study 681 patients with pulmonary TB and show that M. tuberculosis isolates from cases with mild disease consistently induce robust cytokine responses in macrophages across multiple donors. By contrast, bacteria from patients with severe TB do not do so. Secretion of IL-1β is a good surrogate of the differences observed, and thus to classify strains as probable drivers of different TB severities. Furthermore, we demonstrate that M. tuberculosis isolates that induce low levels of IL-1β production can evade macrophage cytosolic surveillance systems, including cGAS and the inflammasome. Isolates exhibiting this evasion strategy carry candidate mutations, generating sigA recognition boxes or affecting components of the ESX-1 secretion system. Therefore, we provide evidence that M. tuberculosis strains manipulate host-pathogen interactions to drive variable TB severities.
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Grants
- The authors thank the excellent support from the i3S scientific platforms, namely Animal facility, Advanced Light Microscopy and BioSciences Screening, member of the national infrastructure PPBI - Portuguese Platform of Bioimaging (PPBI-POCI-01-0145-FEDER-022122). This work was financed by FCT - Fundação para a Ciência e a Tecnologia/ Ministério da Ciência, Tecnologia e Inovação grant POCI-01-0145-FEDER-028955 (to MS) and by the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER) (NORTE-01-0145-FEDER-000013, to MIV, FR, AGC and NSO). IC acknowledges the support of Ministerio de Ciencia, Innovación y Universidades (SAF2016-77346-R) and the European Research Council (638553-TB-ACCELERATE). HNB acknowledges the support of Bolsa D. Manuel de Mello and of the Portuguese Society for Pneumology; AB and MS were also recipients of an International Exchanges Grant from the Royal Society. JS is funded by a research fellow NORTE-01-0145-FEDER-000012; BC and KLF are funded by FCT PhD scholarships SFRH/BD/114403/2016 and SFRH/BD/114405/2016, respectively; MIV is funded by FCT through DL 57/2016 (CRP) and MS through Estimulo Individual ao Emprego Científico.
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Affiliation(s)
- Jeremy Sousa
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Baltazar Cá
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Ana Raquel Maceiras
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Luisa Simões-Costa
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Kaori L Fonseca
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Ana Isabel Fernandes
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Angélica Ramos
- São João Hospital Center & EPIUnit-Institute of Public Health, University of Porto, Porto, Portugal
| | - Teresa Carvalho
- São João Hospital Center & EPIUnit-Institute of Public Health, University of Porto, Porto, Portugal
| | - Leandro Barros
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | | | - Henrique Machado
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Maria Isabel Veiga
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Albel Singh
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Rui Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
| | - António Amorim
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Jorge Vieira
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Cristina P Vieira
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Pedro N S Rodrigues
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - António Gil Castro
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - João Tiago Guimarães
- São João Hospital Center & EPIUnit-Institute of Public Health, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Helder Novais Bastos
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
- São João Hospital Center, Porto, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Iñaki Comas
- Biomedicine Institute of Valencia (CSIC), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Margarida Saraiva
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal.
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Goig GA, Torres-Puente M, Mariner-Llicer C, Villamayor LM, Chiner-Oms Á, Gil-Brusola A, Borrás R, Comas Espadas I. Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics. Bioinformatics 2020; 36:985-989. [PMID: 31580405 PMCID: PMC7703747 DOI: 10.1093/bioinformatics/btz729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/02/2019] [Accepted: 09/25/2019] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Tuberculosis (TB) remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel TB diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study has been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. RESULTS In this work, we used large-scale comparative genomics to identify 40 MTBC-specific loci. We assessed their genetic diversity and physiological features to select 30 that are good targets for diagnostic purposes. Some of these markers could be used to assess the physiological status of the bacilli. Remarkably, none of the most used MTBC markers is in our catalog. Illustrating the translational potential of our work, we develop a specific qPCR assay for quantification and identification of MTBC DNA. Our rational design of targeted molecular assays for TB could be used in many other fields of clinical and basic research. AVAILABILITY AND IMPLEMENTATION The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281/zenodo.3374377. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Galo A Goig
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Carla Mariner-Llicer
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Luis M Villamayor
- Genomics and Health Unit, FISABIO Public Health (CSISP), Valencia 46035, Spain
| | - Álvaro Chiner-Oms
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Ana Gil-Brusola
- Microbiology Service, La Fe University and Polytechnic Hospital, Valencia 46026, Spain
| | - Rafael Borrás
- Microbiology Service, University Clinic Hospital, Valencia 46010, Spain
- Microbiology Department, School of Medicine, University of Valencia, Valencia 46010, Spain
| | - Iñaki Comas Espadas
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
- CIBER in Epidemiology and Public Health, Madrid 28029, Spain
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López MG, Dogba JB, Torres-Puente M, Goig GA, Moreno-Molina M, Villamayor LM, Cadmus S, Comas I. Tuberculosis in Liberia: high multidrug-resistance burden, transmission and diversity modelled by multiple importation events. Microb Genom 2020; 6:e000325. [PMID: 31935183 PMCID: PMC7067037 DOI: 10.1099/mgen.0.000325] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/16/2019] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB) surveillance is scarce in most African countries, even though it is the continent with the greatest disease incidence according to the World Health Organization. Liberia is within the 30 countries with the highest TB burden, probably as a consequence of the long civil war and the recent Ebola outbreak, both crippling the health system and depreciating the TB prevention and control programmes. Due to difficulties working in the country, there is a lack of resistance surveys and bacillus characterization. Here, we use genome sequencing of Mycobacteriumtuberculosis clinical isolates to fill this gap. Our results highlight that the bacillus population structure is dominated by lineage 4 strains that harbour an outstanding genetic diversity, higher than in the rest of Africa as a whole. Coalescent analyses demonstrate that strains currently circulating in Liberia were introduced several times beginning in the early year 600 CE until very recently coinciding with migratory movements associated with the civil war and Ebola epidemics. A higher multidrug-resistant (MDR)-TB frequency (23.5 %) than current estimates was obtained together with non-catalogued drug-resistance mutations. Additionally, 39 % of strains were in genomic clusters revealing that ongoing transmission is a major contribution to the TB burden in the country. Our report emphasizes the importance of TB surveillance and control in African countries where bacillus diversity, MDR-TB prevalence and transmission are coalescing to jeopardize TB control programmes.
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Affiliation(s)
- Mariana G. López
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - John B. Dogba
- Tuberculosis and Brucellosis Laboratories, Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, Ibadan, Nigeria
- Center for Control and Prevention of Zoonoses, University of Ibadan, Ibadan, Nigeria
- Tuberculosis Laboratory, National Public Health Reference Laboratory, National Public Health Institute of Liberia, Margibi, Liberia
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Galo A. Goig
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Miguel Moreno-Molina
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Luis M. Villamayor
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- Unidad Mixta “Infección y Salud Pública” (FISABIO-CSISP), Valencia, Spain
| | - Simeon Cadmus
- Tuberculosis and Brucellosis Laboratories, Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, Ibadan, Nigeria
- Center for Control and Prevention of Zoonoses, University of Ibadan, Ibadan, Nigeria
- Tuberculosis Laboratory, National Public Health Reference Laboratory, National Public Health Institute of Liberia, Margibi, Liberia
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
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Skuce R, Breadon E, Allen A, Milne G, McCormick C, Hughes C, Rutherford D, Smith G, Thompson S, Graham J, Harwood R, Byrne A. Longitudinal dynamics of herd-level Mycobacterium bovis MLVA type surveillance in cattle in Northern Ireland 2003-2016. INFECTION GENETICS AND EVOLUTION 2019; 79:104131. [PMID: 31786341 DOI: 10.1016/j.meegid.2019.104131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/27/2019] [Indexed: 02/02/2023]
Abstract
Investigating genetically-structured diversity in pathogen populations over time is important to better understand disease maintenance and spread. Herd-level surveillance of Mycobacterium bovis genotypes (multi-locus VNTR analysis types, MLVA types) from all culture-confirmed bovine tuberculosis (TB) herd cases was undertaken in Northern Ireland (NI), generating an unparalleled, longitudinal, population-level 14-year survey for this pathogen. Across this population, 295 genetically-distinct M. bovis MLVA types were identified in the 19,717 M. bovis isolates surveyed. Of these, the most frequent was MLVA type 002 (23.0%); 151 MLVA types were represented more than once, in groups ranging from 2 to 4438 isolates. Only 23 MLVA types were isolated in all 14 years. Investigating inter-annual frequency of M. bovis MLVA types, examples of statistically-significant expansions (MLVA types 002, 004, 006, 009 and 027), contractions (MLVA types 001, 007 and 011) and maintenance (MLVA types 003 and 005) were disclosed, during a period of fluctuating bovine TB herd-level incidence at the NI scale. The fixed period frequency distribution of MLVA types remained highly right-skewed. Novel VNTR copy number variant MLVA types (N = 242; an average of 17 per annum) were identified throughout the survey. The MLVA type distribution in the landscape was not random; MLVA types showed statistically-significant geographical localization and strong spatial associations with Divisional Veterinary Office (DVO) regions. There was also evidence of differential risk of particular MLVA types across breeds (Holstein/Friesian vs. other), age-class, and sex and some evidence of an association between the number of animals testing positive for bovine TB during the disclosing test and particular MLVA types, although there was substantial variation.
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Affiliation(s)
- R Skuce
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University Belfast, Belfast BT7 1NN, UK.
| | - E Breadon
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - A Allen
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - G Milne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - C McCormick
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; Veterinary Service and Animal Health Group, Department of Agriculture, Environment and Rural Affairs, Dundonald House, Stormont, Belfast BT4 3SB, UK
| | - C Hughes
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - D Rutherford
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; Faculty of Electrical Engineering, Czech Technical University, Prague, Czech Republic (⁎)current address
| | - G Smith
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - S Thompson
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - J Graham
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - R Harwood
- Veterinary Service and Animal Health Group, Department of Agriculture, Environment and Rural Affairs, Dundonald House, Stormont, Belfast BT4 3SB, UK
| | - A Byrne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University Belfast, Belfast BT7 1NN, UK; One-Health Unit, Surveillance, Animal By-Products and TSEs (SAT), Division Department of Agriculture, Food and Marine (DAFM), Agriculture House, Dublin 2, Ireland
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46
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Cancino-Muñoz I, Gil-Brusola A, Torres-Puente M, Mariner-Llicer C, Dogba J, Akinseye V, Adesokan K, Kwaghe A, Ejeh F, Cadmus S, Comas I. Development and application of affordable SNP typing approaches to genotype Mycobacterium tuberculosis complex strains in low and high burden countries. Sci Rep 2019; 9:15343. [PMID: 31653874 PMCID: PMC6814786 DOI: 10.1038/s41598-019-51326-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/26/2019] [Indexed: 11/21/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) comprises the species that causes tuberculosis (TB) which affects 10 million people every year. A robust classification of species, lineages, and sub-lineages is important to explore associations with drug resistance, epidemiological patterns or clinical outcomes. We present a rapid and easy-to-follow methodology to classify clinical TB samples into the main MTBC clades. Approaches are based on the identification of lineage and sub-lineage diagnostic SNP using a real-time PCR high resolution melting assay and classic Sanger sequencing from low-concentrated, low quality DNA. Thus, suitable for implementation in middle and low-income countries. Once we validated our molecular procedures, we characterized a total of 491 biological samples from human and cattle hosts, representing countries with different TB burden. Overall, we managed to genotype ~95% of all samples despite coming from unpurified and low-concentrated DNA. Our approach also allowed us to detect zoonotic cases in eight human samples from Nigeria. To conclude, the molecular techniques we have developed, are accurate, discriminative and reproducible. Furthermore, it costs less than other classic typing methods, resulting in an affordable alternative method in TB laboratories.
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Affiliation(s)
- Irving Cancino-Muñoz
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- FISABIO Public Health, Genomics and Health Unit, Valencia, Spain
| | - Ana Gil-Brusola
- Hospital Universitari I Politècnic La Fe, Microbiology Department, Valencia, Spain
| | | | | | - John Dogba
- University of Ibadan, Department of Veterinary Public Health & Preventive Medicine, Ibadan, Nigeria
- University of Ibadan, Centre for Control and Prevention of Zoonosis, Ibadan, Nigeria
| | - Victor Akinseye
- University of Ibadan, Department of Veterinary Public Health & Preventive Medicine, Ibadan, Nigeria
| | - Kehinde Adesokan
- University of Ibadan, Department of Veterinary Public Health & Preventive Medicine, Ibadan, Nigeria
| | - Ayi Kwaghe
- Federal Ministry of Agriculture and Rural Development, Department of Veterinary and Pest Control Services, Garki, Nigeria
| | - Francis Ejeh
- University of Maiduguri, Department of Veterinary Microbiology, Maiduguri, Nigeria
| | - Simeon Cadmus
- University of Ibadan, Department of Veterinary Public Health & Preventive Medicine, Ibadan, Nigeria
- University of Ibadan, Centre for Control and Prevention of Zoonosis, Ibadan, Nigeria
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain.
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47
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Xu Y, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Borrás R, Borrás-Máñez M, Bosque M, Camarena JJ, Colomer-Roig E, Colomina J, Escribano I, Esparcia-Rodríguez O, Gil-Brusola A, Gimeno C, Gimeno-Gascón A, Gomila-Sard B, González-Granda D, Gonzalo-Jiménez N, Guna-Serrano MR, López-Hontangas JL, Martín-González C, Moreno-Muñoz R, Navarro D, Navarro M, Orta N, Pérez E, Prat J, Rodríguez JC, Ruiz-García MM, Vanaclocha H, Colijn C, Comas I. High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain. PLoS Med 2019; 16:e1002961. [PMID: 31671150 PMCID: PMC6822721 DOI: 10.1371/journal.pmed.1002961] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/07/2019] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Whole genome sequencing provides better delineation of transmission clusters in Mycobacterium tuberculosis than traditional methods. However, its ability to reveal individual transmission links within clusters is limited. Here, we used a 2-step approach based on Bayesian transmission reconstruction to (1) identify likely index and missing cases, (2) determine risk factors associated with transmitters, and (3) estimate when transmission happened. METHODS AND FINDINGS We developed our transmission reconstruction method using genomic and epidemiological data from a population-based study from Valencia Region, Spain. Tuberculosis (TB) incidence during the study period was 8.4 cases per 100,000 people. While the study is ongoing, the sampling frame for this work includes notified TB cases between 1 January 2014 and 31 December 2016. We identified a total of 21 transmission clusters that fulfilled the criteria for analysis. These contained a total of 117 individuals diagnosed with active TB (109 with epidemiological data). Demographic characteristics of the study population were as follows: 80/109 (73%) individuals were Spanish-born, 76/109 (70%) individuals were men, and the mean age was 42.51 years (SD 18.46). We found that 66/109 (61%) TB patients were sputum positive at diagnosis, and 10/109 (9%) were HIV positive. We used the data to reveal individual transmission links, and to identify index cases, missing cases, likely transmitters, and associated transmission risk factors. Our Bayesian inference approach suggests that at least 60% of index cases are likely misidentified by local public health. Our data also suggest that factors associated with likely transmitters are different to those of simply being in a transmission cluster, highlighting the importance of differentiating between these 2 phenomena. Our data suggest that type 2 diabetes mellitus is a risk factor associated with being a transmitter (odds ratio 0.19 [95% CI 0.02-1.10], p < 0.003). Finally, we used the most likely timing for transmission events to study when TB transmission occurred; we identified that 5/14 (35.7%) cases likely transmitted TB well before symptom onset, and these were largely sputum negative at diagnosis. Limited within-cluster diversity does not allow us to extrapolate our findings to the whole TB population in Valencia Region. CONCLUSIONS In this study, we found that index cases are often misidentified, with downstream consequences for epidemiological investigations because likely transmitters can be missed. Our findings regarding inferred transmission timing suggest that TB transmission can occur before patient symptom onset, suggesting also that TB transmits during sub-clinical disease. This result has direct implications for diagnosing TB and reducing transmission. Overall, we show that a transition to individual-based genomic epidemiology will likely close some of the knowledge gaps in TB transmission and may redirect efforts towards cost-effective contact investigations for improved TB control.
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Affiliation(s)
- Yuanwei Xu
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, United Kingdom
| | - Irving Cancino-Muñoz
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Manuela Torres-Puente
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - Rafael Borrás
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - María Borrás-Máñez
- Microbiology and Parasitology Service, Hospital Universitario de La Ribera, Alzira, Spain
| | | | - Juan J. Camarena
- Microbiology Service, Hospital Universitario Dr. Peset, Valencia, Spain
| | - Ester Colomer-Roig
- Genomics and Health Unit, FISABIO Public Health, Valencia, Spain
- Microbiology Service, Hospital Universitario Dr. Peset, Valencia, Spain
| | - Javier Colomina
- Microbiology and Parasitology Service, Hospital Universitario de La Ribera, Alzira, Spain
| | - Isabel Escribano
- Microbiology Laboratory, Hospital Virgen de los Lírios, Alcoy, Spain
| | | | - Ana Gil-Brusola
- Microbiology Service, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Concepción Gimeno
- Microbiology Service, Hospital General Universitario de Valencia, Valencia, Spain
| | | | - Bárbara Gomila-Sard
- Microbiology Service, Hospital General Universitario de Castellón, Castellon, Spain
| | | | | | | | | | - Coral Martín-González
- Microbiology Service, Hospital Universitario de San Juan de Alicante, Alicante, Spain
| | - Rosario Moreno-Muñoz
- Microbiology Service, Hospital General Universitario de Castellón, Castellon, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - María Navarro
- Microbiology Service, Hospital de la Vega Baixa, Orihuela, Spain
| | - Nieves Orta
- Microbiology Service, Hospital San Francesc de Borja, Gandía, Spain
| | - Elvira Pérez
- Subdirección General de Epidemiología y Vigilancia de la Salud, Dirección General de Salud Pública, Valencia, Spain
| | - Josep Prat
- Microbiology Service, Hospital de Sagunto, Sagunto, Spain
| | | | | | - Herme Vanaclocha
- Subdirección General de Epidemiología y Vigilancia de la Salud, Dirección General de Salud Pública, Valencia, Spain
| | - Caroline Colijn
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, United Kingdom
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (CC); (IC)
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
- * E-mail: (CC); (IC)
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48
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Chiner-Oms Á, Berney M, Boinett C, González-Candelas F, Young DB, Gagneux S, Jacobs WR, Parkhill J, Cortes T, Comas I. Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex. Nat Commun 2019; 10:3994. [PMID: 31488832 PMCID: PMC6728331 DOI: 10.1038/s41467-019-11948-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) members display different host-specificities and virulence phenotypes. Here, we have performed a comprehensive RNAseq and methylome analysis of the main clades of the MTBC and discovered unique transcriptional profiles. The majority of genes differentially expressed between the clades encode proteins involved in host interaction and metabolic functions. A significant fraction of changes in gene expression can be explained by positive selection on single mutations that either create or disrupt transcriptional start sites (TSS). Furthermore, we show that clinical strains have different methyltransferases inactivated and thus different methylation patterns. Under the tested conditions, differential methylation has a minor direct role on transcriptomic differences between strains. However, disruption of a methyltransferase in one clinical strain revealed important expression differences suggesting indirect mechanisms of expression regulation. Our study demonstrates that variation in transcriptional profiles are mainly due to TSS mutations and have likely evolved due to differences in host characteristics.
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Affiliation(s)
- Álvaro Chiner-Oms
- Unidad Mixta "Infección y Salud Pública" FISABIO-CSISP/Universidad de Valencia, Instituto de Biología Integrativa de Sistemas-I2SysBio, Valencia, Spain.,Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, Spain
| | - Michael Berney
- Department of Microbiology and Immunology and Department of Molecular Genetics, Albert Einstein College of Medicine, New York, USA
| | - Christine Boinett
- Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Fernando González-Candelas
- Unidad Mixta "Infección y Salud Pública" FISABIO-CSISP/Universidad de Valencia, Instituto de Biología Integrativa de Sistemas-I2SysBio, Valencia, Spain.,CIBER en Epidemiología y Salud Pública, Valencia, Spain
| | | | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - William R Jacobs
- Department of Microbiology and Immunology and Department of Molecular Genetics, Albert Einstein College of Medicine, New York, USA
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Mandingley Road, Cambiddge, CB3 OES, UK
| | - Teresa Cortes
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, Spain. .,CIBER en Epidemiología y Salud Pública, Valencia, Spain.
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49
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Direct transmission of within-host Mycobacterium tuberculosis diversity to secondary cases can lead to variable between-host heterogeneity without de novo mutation: A genomic investigation. EBioMedicine 2019; 47:293-300. [PMID: 31420303 PMCID: PMC6796532 DOI: 10.1016/j.ebiom.2019.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Whole genome sequencing (WGS) has enabled the development of new approaches to track Mycobacterium tuberculosis (Mtb) transmission between tuberculosis (TB) cases but its utility may be challenged by the discovery that Mtb diversifies within hosts. Nevertheless, there is limited data on the presence and degree of within-host evolution. METHODS We profiled a well-documented Mtb transmission cluster with three pulmonary TB cases to investigate within-host evolution and describe its impact on recent transmission estimates. We used deep sequencing to track minority allele frequencies (<50·0% abundance) during transmission and standard treatment. FINDINGS Pre-treatment (n = 3) and serial samples collected over 2 months of antibiotic treatment (n = 16) from all three cases were analysed. Consistent with the epidemiological data, zero fixed SNP separated all genomes. However, we identified six subclones between the three cases with an allele frequency ranging from 35·0% to 100·0% across sampling intervals. Five subclones were identified within the index case pre-treatment and shared with one secondary case, while only the dominant clone was observed in the other secondary case. By tracking the frequency of these heterogeneous alleles over the two-month therapy, we observed distinct signatures of drift and negative selection, but limited evidence for de novo mutations, even under drug pressure. INTERPRETATION We document within-host Mtb diversity in an index case, which led to transmission of minority alleles to a secondary case. Incorporating data on heterogeneous alleles may refine our understanding of Mtb transmission dynamics. However, more evidence is needed on the role of transmission bottleneck on observed heterogeneity between cases.
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